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ENCSR300QFQ

ENCSR ENCODE
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RNA-seq on K562 cells treated with an shRNA knockdown against TRIM56. (TRIM56_BGKLV21)

Organism: Homo sapiens
Experiment Types:
shRNA RNA-seq
Status: released
Contact: Brenton Graveley, UConn

Summary

shRNA RNA-seq of TRIM56 in Homo sapiens K562 expressing RNAi targeting H. sapiens TRIM56

Overall Design

RNA-seq on K562 cells treated with an shRNA knockdown against TRIM56. (TRIM56_BGKLV21)

Analysis

View Data Processing
Analysis page is available for ENCSR300QFQ.

Dataset Citations (3)

PubMed citation (PMID 32728046)
PubMed citation (PMID 32727537)
A large-scale binding and functional map of human RNA-binding proteins.
PMID 32728246 · 2020 · Nature
Eric L Van Nostrand, Peter Freese, Gabriel A Pratt, Xiaofeng Wang, Xintao Wei, Rui Xiao, Steven M Blue, Jia-Yu Chen, Neal A L Cody, Daniel Dominguez, Sara Olson, Balaji Sundararaman, Lijun Zhan, Cassandra Bazile, Louis Philip Benoit Bouvrette, Julie Bergalet, Michael O Duff, Keri E Garcia, Chelsea Gelboin-Burkhart, Myles Hochman, Nicole J Lambert, Hairi Li, Michael P McGurk, Thai B Nguyen, Tsultrim Palden, Ines Rabano, Shashank Sathe, Rebecca Stanton, Amanda Su, Ruth Wang, Brian A Yee, Bing Zhou, Ashley L Louie, Stefan Aigner, Xiang-Dong Fu, Eric Lécuyer, Christopher B Burge, Brenton R Graveley, Gene W Yeo

ENCODE Metadata

Total file size: 84.2 GB
Assay: shRNA RNA-seq
Target: TRIM56
Biosample: Homo sapiens K562 expressing RNAi targeting H. sapiens TRIM56
Files: 92
Unique ENC file IDs: 92
File Formats
bigWig (48) tsv (19) bam (18) fastq (4) tar (3)
Output types (11)
alignments (12) minus strand signal of all reads (12) minus strand signal of unique reads (12) plus strand signal of all reads (12) plus strand signal of unique reads (12) transcript quantifications (8) gene quantifications (6) transcriptome alignments (6) differential expression quantifications (5) reads (4) differential splicing quantifications (3)

Linked Publications (1)

A large-scale binding and functional map of human RNA-binding proteins.
Nature · 2020

Data Files (92)

Accession File Name Stored Type Output Type Mapping Assembly Size Download
ENCFF078BXG ENCFF078BXG.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 3.8 GB link
ENCFF182JXJ ENCFF182JXJ.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 4.6 GB link
ENCFF942FAX ENCFF942FAX.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 3.4 GB link
ENCFF977JMX ENCFF977JMX.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 2.9 GB link
ENCFF123DTH ENCFF123DTH.bam bam (alignments); assembly: GRCh38; genome annotation: V29 alignments GRCh38 3.4 GB link
ENCFF602PJC ENCFF602PJC.bam bam (alignments); assembly: GRCh38; genome annotation: V29 alignments GRCh38 4.6 GB link
ENCFF463OAJ ENCFF463OAJ.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 3.8 GB link
ENCFF526EKZ ENCFF526EKZ.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 3.3 GB link
ENCFF530WWM ENCFF530WWM.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 2.8 GB link
ENCFF641IIS ENCFF641IIS.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 4.5 GB link
ENCFF644KGR ENCFF644KGR.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 3.8 GB link
ENCFF905QAH ENCFF905QAH.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 2.8 GB link
ENCFF215FPD ENCFF215FPD.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V24 transcriptome alignments GRCh38 3.9 GB link
ENCFF593KCE ENCFF593KCE.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V24 transcriptome alignments GRCh38 5.3 GB link
ENCFF530KMZ ENCFF530KMZ.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V29 transcriptome alignments GRCh38 4.3 GB link
ENCFF925DMT ENCFF925DMT.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V29 transcriptome alignments GRCh38 5.9 GB link
ENCFF295HQX ENCFF295HQX.bam bam (transcriptome alignments); assembly: hg19; genome annotation: V19 transcriptome alignments hg19 3.8 GB link
ENCFF759LRR ENCFF759LRR.bam bam (transcriptome alignments); assembly: hg19; genome annotation: V19 transcriptome alignments hg19 5.3 GB link
ENCFF244PSC ENCFF244PSC.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 72.5 MB link
ENCFF417GAB ENCFF417GAB.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 64.3 MB link
ENCFF516VZK ENCFF516VZK.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 81.3 MB link
ENCFF730KRX ENCFF730KRX.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 71.8 MB link
ENCFF520UIY ENCFF520UIY.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V29 minus strand signal of all reads GRCh38 81.3 MB link
ENCFF567UPH ENCFF567UPH.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V29 minus strand signal of all reads GRCh38 71.9 MB link
ENCFF005OYT ENCFF005OYT.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 80.9 MB link
ENCFF265TMC ENCFF265TMC.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 70.4 MB link
ENCFF380TBW ENCFF380TBW.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 65.3 MB link
ENCFF384IZJ ENCFF384IZJ.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 60.0 MB link
ENCFF621ALY ENCFF621ALY.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 70.4 MB link
ENCFF692WRP ENCFF692WRP.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 73.7 MB link
ENCFF064UYB ENCFF064UYB.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 72.2 MB link
ENCFF448OEG ENCFF448OEG.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 68.2 MB link
ENCFF513ZNX ENCFF513ZNX.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 59.9 MB link
ENCFF668IJE ENCFF668IJE.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 63.1 MB link
ENCFF746JSB ENCFF746JSB.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 minus strand signal of unique reads GRCh38 72.0 MB link
ENCFF855XJY ENCFF855XJY.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 minus strand signal of unique reads GRCh38 63.1 MB link
ENCFF126SBS ENCFF126SBS.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 71.6 MB link
ENCFF153XAH ENCFF153XAH.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 60.1 MB link
ENCFF546RNB ENCFF546RNB.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 63.3 MB link
ENCFF664RZQ ENCFF664RZQ.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 68.2 MB link
ENCFF768FDW ENCFF768FDW.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 63.4 MB link
ENCFF924RMF ENCFF924RMF.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 55.8 MB link
ENCFF687SMY ENCFF687SMY.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 65.3 MB link
ENCFF788XPX ENCFF788XPX.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 72.9 MB link
ENCFF917TWS ENCFF917TWS.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 73.4 MB link
ENCFF978UFG ENCFF978UFG.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 82.3 MB link
ENCFF092UHX ENCFF092UHX.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V29 plus strand signal of all reads GRCh38 82.4 MB link
ENCFF639POE ENCFF639POE.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V29 plus strand signal of all reads GRCh38 72.9 MB link
ENCFF013IJB ENCFF013IJB.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 75.1 MB link
ENCFF017ZSS ENCFF017ZSS.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 71.5 MB link
ENCFF220FVT ENCFF220FVT.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 71.8 MB link
ENCFF574DNX ENCFF574DNX.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 61.2 MB link
ENCFF632PAX ENCFF632PAX.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 66.6 MB link
ENCFF903PJA ENCFF903PJA.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 82.0 MB link
ENCFF367ZCC ENCFF367ZCC.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 64.7 MB link
ENCFF901JYO ENCFF901JYO.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 69.7 MB link
ENCFF953HPC ENCFF953HPC.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 61.3 MB link
ENCFF956VEM ENCFF956VEM.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 73.8 MB link
ENCFF253YNM ENCFF253YNM.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 plus strand signal of unique reads GRCh38 73.7 MB link
ENCFF788IQZ ENCFF788IQZ.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 plus strand signal of unique reads GRCh38 64.7 MB link
ENCFF003UJH ENCFF003UJH.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 65.1 MB link
ENCFF047QSY ENCFF047QSY.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 65.1 MB link
ENCFF142NGK ENCFF142NGK.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 70.0 MB link
ENCFF177DBS ENCFF177DBS.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 61.8 MB link
ENCFF497NZC ENCFF497NZC.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 57.4 MB link
ENCFF985ECS ENCFF985ECS.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 73.5 MB link
ENCFF711JIW ENCFF711JIW.fastq fastq (reads) reads 2.4 GB link
ENCFF760FBT ENCFF760FBT.fastq fastq (reads) reads 1.7 GB link
ENCFF915WOP ENCFF915WOP.fastq fastq (reads) reads 2.6 GB link
ENCFF959BUP ENCFF959BUP.fastq fastq (reads) reads 1.9 GB link
ENCFF549CVO ENCFF549CVO.tar tar (differential splicing quantifications); assembly: hg19; genome annotation: V19 differential splicing quantifications hg19 3.8 MB link
ENCFF794ZZH ENCFF794ZZH.tar tar (differential splicing quantifications); assembly: hg19; genome annotation: V19 differential splicing quantifications hg19 14.1 MB link
ENCFF979UMH ENCFF979UMH.tar tar (differential splicing quantifications); assembly: hg19; genome annotation: V19 differential splicing quantifications hg19 3.2 MB link
ENCFF006DPZ ENCFF006DPZ.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 2.9 MB link
ENCFF079LOC ENCFF079LOC.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 5.6 MB link
ENCFF099ZDX ENCFF099ZDX.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 4.3 MB link
ENCFF249MDX ENCFF249MDX.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 1.7 MB link
ENCFF488VXR ENCFF488VXR.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 1.9 MB link
ENCFF595VCS ENCFF595VCS.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V24 gene quantifications GRCh38 9.4 MB link
ENCFF670WYH ENCFF670WYH.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V24 gene quantifications GRCh38 9.4 MB link
ENCFF083OXA ENCFF083OXA.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V29 gene quantifications GRCh38 10.4 MB link
ENCFF247IET ENCFF247IET.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V29 gene quantifications GRCh38 10.4 MB link
ENCFF561BHJ ENCFF561BHJ.tsv tsv (gene quantifications); assembly: hg19; genome annotation: V19 gene quantifications hg19 9.1 MB link
ENCFF793TCY ENCFF793TCY.tsv tsv (gene quantifications); assembly: hg19; genome annotation: V19 gene quantifications hg19 9.1 MB link
ENCFF049VAO ENCFF049VAO.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V24 transcript quantifications GRCh38 25.3 MB link
ENCFF444NNT ENCFF444NNT.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V24 transcript quantifications GRCh38 25.3 MB link
ENCFF203MAR ENCFF203MAR.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 29.8 MB link
ENCFF409ROU ENCFF409ROU.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 27.3 MB link
ENCFF575WLT ENCFF575WLT.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 27.3 MB link
ENCFF888RVW ENCFF888RVW.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 29.8 MB link
ENCFF068ERK ENCFF068ERK.tsv tsv (transcript quantifications); assembly: hg19; genome annotation: V19 transcript quantifications hg19 24.9 MB link
ENCFF976STP ENCFF976STP.tsv tsv (transcript quantifications); assembly: hg19; genome annotation: V19 transcript quantifications hg19 24.9 MB link